Full information on isolate MM0011CK (id:852)
Provenance/primary metadata
- id
- 852
- isolate
- MM0011CK
- aliases
- A1_Mm_MM011K; L3; MM0011; MM011K
- clade
- P1
- species
- borgpetersenii
- serogroup
- Ballum
- serovar
- Ballum
- isolation year
- 2016
- sequencing year
- 2018
- passage
- 0
- world region
- Australia and New Zealand
- country
- New Zealand
- city
- Manawatu-Wanganui
- host
- house mouse
- sample type
- kidney
- source lab
- mEpiLab Massey University
- living area
- rural
- clinical conditions
- subclinical
- comments
- Species=Mus musculus
- sender
- Marie Moinet, Massey University, New Zealand
- curator
- Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
- update history
- 16 updates show details
- date entered
- 2019-03-11
- datestamp
- 2024-04-17
Sequence bin
- contigs
- 161
- total length
- 3,894,764 bp
- max length
- 190,752 bp
- mean length
- 24,192 bp
- N50
- 43,982
- L50
- 25
- N90
- 14,977
- L90
- 84
- N95
- 9,300
- L95
- 99
- %GC
- 40.02
- Ns
- 0
- gaps
- 0
- loci tagged
- 602
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Annotation quality metrics
Scheme completion
| Scheme | Scheme loci | Designated loci | Annotation | |
|---|---|---|---|---|
| Score | Status | |||
| cgMLST | 545 | 543 | 99 | |
Similar isolates (determined by classification schemes)
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 15 (118 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (118 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 14 (80 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 13 (80 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 16 (80 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 13 (80 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (118 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (118 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (118 isolates) |
| Cluster_40_cgMLST | cgMLST | Single-linkage | 40 | experimental | 15 (118 isolates) |
| Test-50 | cgMLST | Single-linkage | 50 | experimental | 15 (118 isolates) |
| Test-110 | cgMLST | Single-linkage | 110 | experimental | 14 (80 isolates) |
| Test-150 | cgMLST | Single-linkage | 150 | experimental | 13 (80 isolates) |
| Test-20 | cgMLST | Single-linkage | 20 | experimental | 16 (80 isolates) |
| Test-200 | cgMLST | Single-linkage | 200 | experimental | 13 (80 isolates) |
| Test-30 | cgMLST | Single-linkage | 30 | experimental | 15 (118 isolates) |
| Test-300 | cgMLST | Single-linkage | 300 | experimental | 8 (146 isolates) |
| Test-60 | cgMLST | Single-linkage | 60 | experimental | 15 (118 isolates) |
| Test-80 | cgMLST | Single-linkage | 80 | experimental | 14 (118 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
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